I have been using the following class in my game, one I created on my own to fit my campaign. Most of it was adapted from the Bard class, so keep in mind it is meant to be used as a bard-like class rather than a true spellcasting class. Please look it over carefully and check for problems you find in the class as well as suggestions for improving it. I cut and pasted from my website so excuse any errors from transmission. Also keep in mind that it only is up to level 13 so far, so allow for another 7 levels.

Alchemist

Considered mystical and magical, the arts of the high sciences are strange to those who are not familiar with them. Mathmatics and physics are the alchemists weapons, along with chemistry and patience. "The attributes without mirror the powers within"(Secret of the sixth magic, by Lyndon Hardy, preface). By unlocking these powers, the alchemist puts the power of nature at his command. Adventures: While most alchemists stay in their laboratory, some realize that there may be more for them out in the world, and they do not have the patience to let others bring back what they feel might yeild results. These alchemists join parties to search out new discoveries.Alignment: Harnessing the power of nature and science, so an Alchemist must be Lawful, but neither good, evil or neutrality affects his ability to do his job.Background: An alchemist almost always comes from intelligent parents who are also secure in their financial stability. It takes a supportive network of encouragement, finances and genetics to bring this rare breed to life and keep them workingHit dice: 1d6

Weapon and Armor Profficiencies: Alchemists are profficient with all simple weapons, as well as the light pick and light hammer. They are profficient with light armor and shields. Note for any armor heavier than light armor the Alchemist stands a chance for spell failure.

Spells: Working with magic, the Alchemist becomes familiar with a few simple spells to help them along. He casts spells from the wizard spell list, but he must prepare them ahead of time as a wizard would. An Alchemist recieves bonus spells based on his intelligence score. An Alchemist creates a spellbooks like a wizard does starting at level 2. The difficulty class against an Alchemist's spells is 10 + the spell level + the Alchemists Intelligence modifier. To learn to cast a spell, an Alchemist must have an Intelligence score of at least 10 + the spell level (Int 10 for 0 cantrips).

Spellbook: An Alchemist must study his spellbook each day to prepare his spells. He cannot prepare any spell not recorder in his spellbook. When an Alchemist gains 2nd level, they create a spellbook containing 6 0-level spells plus three 1st level spells of their choice. At each new alchemist level the Alchemist gains two new spells of any spell level or levels that the Alchemist can cast from their spellbook (see example page 57 AD&D 3.5 ed. PHB).

Level

BAB

FORT

REF

WILL

Special Abilities

1

+0

+2

+0

+0

Skill Focus(craft), Scientific Knowledge

2

+1

+3

+0

+0

3

+2

+3

+1

+1

Use Poison Feat*

4

+3

+4

+1

+1

Brew potion, Skilled analysis

5

+3

+4

+1

+1

Superior Alloy

6

+4

+5

+2

+2

Scribe Scroll, skill focus Craft(any)

7

+5

+5

+2

+2

8

+6/+1

+6

+2

+2

Master Alloy

9

+6/+1

+6

+3

+3

Bonus item creation feat

10

+7/+2

+7

+3

+3

Brew Greater potion

11

+7/+2

+7

+4

+4

Major

12

+8/+3

+8

+4

+4

Breakthrough

13

+8/+3

+8

+5

+5

Spell Use: Use the bard spells list for spells known and spells per day, though the spells should be chosen from the Wizard/sorceror spell list.Scientific Knowledge: The Alchemist tends to pick up stray bits of knowledge from research, anchient tomes, and discourse with other Alchemists and wizards. Anytime an Alchemist desires to know anything about metals, chemicals, ore, dust, or other science related fields he may make a special Scientific knowledge check with a bonus equal to his Alchemist level + his Intelligence modifier (If the Alchemist has 5 or more ranks in Craft(Alchemy), he gains a +2 bonus on this check.). This functions like a Bardic knowledge check, but in the fields mentioned. This can be used to identify potions with a DC 20 check. Skill Focus: The alchemist gets skill focus in any craft skill as a bonus feat. This skill must have been used at least a few times prior to gaining this ability (example a weaponsmith who has never touched a brick cannot gain skill focus(stonemasonry).Poison Use: As the assassin ability, however good and neutral Alchemists cannot create or use deadly poison, only debilitating poison. Any Poison which causes constitution damage that is created or used is considered an evil act in this society(game). Refer to the DMG for poison rules, creation, etc.Brew potion: as the featSkilled Analysis: The Alchemist may take 10 on any craft(alchemy) check even while distraced. If used while combat is going on, it is a standard action that does not incur attacks of opportunity.Superior Alloy: After this ability is gained, treat the creation of any weapon, armor or other metal item as if the alchemist was creating a masterwork item. If the checks are successful, the alchemist has created a masterwork item, but without the added cost.Scribe Scroll: The Alchemist gains the Scribe scroll feat as a bonus featMaster alloy: Treat any metal weapon, armor or other item the Alchemist creates as a masterpiece item. If the check is successful, the alchemist creates the item as a masterpeice without the cost. See the Wheel of time book for rules on masterwork items.Brew Greater Potion: As brew potion but the potion can hold up to a 5th level spell.Major: The Alcemist of 11th level must choose a course of major study. This Major must be chosen, can only be chosen once and can not be changed. The Alchemist recieves a +2 focus bonus to any Craft, knowledge, or proffession(scientist, alchemist, other with dm approval)check related to his Major. No more ranks can be taken in craft, knowledge, or proffession checks related to other Majors (though the old ranks still apply. Majors include;Biology(human): The study of the physiology and psychology, both current and developmental, of Humans, Dwarves, Elves, and all other humanoids.Engineering(mechanical): The study of devices, gadgets and mechanisms. Ranks in Craft(alchemy) may still be taken.Engineering(Sturctural): The study of buildings, arches, walls and other forms of construction. Ranks in Craft(alchemy) may still be taken.Chemistry: The study of metals, fluids, substances, and other chemical mixings. Ranks of craft(weapons) or Craft(armor) may still be taken.Botany: The study of trees, vines, shrubs, herbs and other plants. Physics: The study of motion, countermotion, inertia and gravity. Breakthrough: You have made an accidental breakthrough relating to your major.Biology: You have discovered a combination of protiens and liquids that when injested with food provide a +1 enhancement bonus to Strength, constitution, or dexterity for a period of 24 hours. You can make this substance as often as desired, but it takes 5 minutes per portion and costs 1 gp per portion.Engineering(mechanical): You have discovered a clever mechanism that adds functionality to a weapon you are profficient with. This can only be included in newly forged weapons but adds an ability worth a +1 bonus to the weapon (including a +1 bonus if desired). It costs 200 gp(plus the costs of the weapon) to make the weapon in this manner and takes 8 hours, but can be done as often as able. This is a permanent modifier, and while nonmagical, stacks with everything.Engineering(Sturctural): Your knowledge of structure allows you to build or oversee the building of walls which had an extra 5 points of hardness and 10 extra hit points. It costs 10 extra gp per 10 foot section and takes 1 hour longer, but is permanent.Chemistry: You develop an acid which deals 5 points of damage per round for 3 rounds, and ignores the hardness of objects. While the acid only costs 5 gp per batch, specially made glass jars to hold it cost 10gp each.Botany: You have developed a strain of one plant that is twice as fruitful. Any field which recieves the seed of your plant will be twice as fruitful. This process costs nothing, but each field can recieve this benefit only once (though it lasts until the field is destroyed).Physics: Your knowledge of impact and interia allow you to design a weapon for yourself which does an extra 1d6 points of damage. This must be a blunt or ranged weapon, but this damage stacks with everything. Double the costs of the weapon.

Maybe have the Breakthrough abilities be a list of things they can choose from at various levels, kinda like the rogue's special abilities (or the Loremasters special abilities)? It seems kinda odd that every alchemist would have a "breakthrough" that does the exact same thing. OR, maybe they figure out a way to apply a 1st level spell or something, so the player really can make his own unique breakthrough.

Have you looked at the Eberron artificer? It seems kinda similar in flavor and abilities, so that could give you some ideas. Something similar to the infusions or whatever might make more sense than having a spellbook.

I think the coolest idea in alchemy is to be able to make powerful potions on the fly just by gathering random leaves, or to be able to mix potions together to get some really cool effect. Would something like those fit your concept of the class?

i'm not sure why this character knows how to use armor, he seems like a book worm. also the spell list should be custom. i see no reason why this character ought to have magic missile. a potion maker ought to have access to some healing spells. i'd adapt the bard spell list. go through and when you come to a spell that's too badry (hideous laughter?) sub it for something more nerdy. i'd give brew potion at first level and have a secondary spell list that the character can use that can ONLY be brewed into potions. charm person? no. brew a love potion? yes.